Variant report

Variant	rs10207628
Chromosome Location	chr2:127852021-127852022
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:127846603..127849237-chr2:127850068..127853450,3	K562	blood:
2	chr2:127843180..127845570-chr2:127848864..127852714,3	MCF-7	breast:
3	chr2:127839430..127842816-chr2:127848432..127852029,4	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10166461	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10182292	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10198934	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10207708	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887884	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389409	0.94[ASN][1000 genomes]
rs13400939	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13410629	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1530047	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014923	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6743470	1.00[CHB][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs749006	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7566991	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7575209	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7594230	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1003730	chr2:127794288-127860830	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1003461	chr2:127794288-127862257	Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv516759	chr2:127796666-127859441	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1000994	chr2:127797089-127860830	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv1825024	chr2:127798138-127864285	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv459241	chr2:127800981-127868435	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv583033	chr2:127800981-127868435	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv875011	chr2:127800981-127868435	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv875012	chr2:127800981-127895573	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1002673	chr2:127801964-127860830	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv1010577	chr2:127801964-127862257	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1011224	chr2:127802375-127860830	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1003887	chr2:127802375-127862257	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1009309	chr2:127802730-127862257	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv1014290	chr2:127805366-127860830	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv1010084	chr2:127805366-127862257	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv997855	chr2:127806424-127857946	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv1001673	chr2:127810478-127858634	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv1002124	chr2:127810478-127860830	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv1005423	chr2:127814781-127857751	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv997847	chr2:127814781-127858634	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	nsv1014118	chr2:127814781-127860830	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
25	nsv999224	chr2:127821207-127860830	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	nsv1001064	chr2:127828941-127862257	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
28	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
29	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
30	nsv1005149	chr2:127841930-127880106	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
31	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
32	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
33	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Psychosis and Alzheimer's disease	22005930	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10207628	BIN1	cis	Esophagus Muscularis	GTEx
rs10207628	UGGT1	cis	parietal	SCAN
rs10207628	SMPD4	cis	cerebellum	SCAN
rs10207628	ERCC3	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127835400-127853200	Enhancers	Primary hematopoietic stem cells	blood
2	chr2:127839400-127852800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:127842200-127857000	Enhancers	Psoas Muscle	Psoas
4	chr2:127845200-127859400	Enhancers	Brain Anterior Caudate	brain
5	chr2:127845400-127858400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:127845600-127852200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:127845600-127853200	Enhancers	Brain Cingulate Gyrus	brain
8	chr2:127846000-127852200	Weak transcription	Ovary	ovary
9	chr2:127846000-127852200	Weak transcription	Pancreas	Pancrea
10	chr2:127846000-127852200	Weak transcription	NHLF	lung
11	chr2:127846000-127854000	Weak transcription	Right Atrium	heart
12	chr2:127846000-127856000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:127846800-127853600	Genic enhancers	Fetal Muscle Leg	muscle
14	chr2:127846800-127856800	Genic enhancers	Fetal Intestine Small	intestine
15	chr2:127848000-127857200	Enhancers	HSMMtube	muscle
16	chr2:127848400-127853200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:127848400-127858400	Genic enhancers	Fetal Muscle Trunk	muscle
18	chr2:127848800-127855200	Enhancers	Spleen	Spleen
19	chr2:127848800-127857000	Enhancers	Brain Angular Gyrus	brain
20	chr2:127849800-127852400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:127849800-127853000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr2:127849800-127854600	Enhancers	Fetal Thymus	thymus
23	chr2:127849800-127857000	Bivalent Enhancer	Placenta	Placenta
24	chr2:127850000-127853000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr2:127850000-127853400	Enhancers	Lung	lung
26	chr2:127850000-127856200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr2:127850000-127856600	Enhancers	Fetal Intestine Large	intestine
28	chr2:127850200-127853400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr2:127850200-127853600	Enhancers	A549	lung
30	chr2:127850200-127854600	Genic enhancers	Fetal Stomach	stomach
31	chr2:127850400-127852600	Weak transcription	Fetal Brain Male	brain
32	chr2:127850400-127853200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:127850600-127852200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:127850600-127853400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:127850600-127854200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr2:127850600-127854200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr2:127850600-127856800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:127850600-127857000	Enhancers	Adipose Nuclei	Adipose
39	chr2:127850800-127852600	Enhancers	HUVEC	blood vessel
40	chr2:127850800-127853400	Enhancers	Fetal Kidney	kidney
41	chr2:127850800-127854200	Enhancers	Fetal Lung	lung
42	chr2:127850800-127856000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:127851000-127852200	Enhancers	Hela-S3	cervix
44	chr2:127851000-127852200	Weak transcription	NH-A	brain
45	chr2:127851000-127853200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:127851000-127853800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:127851000-127858200	Enhancers	Duodenum Mucosa	Duodenum
48	chr2:127851200-127852200	Weak transcription	NHEK	skin
49	chr2:127851200-127853200	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr2:127851200-127853600	Enhancers	Duodenum Smooth Muscle	Duodenum

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